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4,753 results for “SHAPE”
Tuning cell behavior with nanoparticle shape
We investigated how the shape of polymeric vesicles, made by the exact same material, impacts the replication activity and metabolic state of both cancer and non-cancer cell types. First, we isolated discrete geometrical structures (spheres and tubes) from a heterogeneous sample using density-gradient centrifugation. Then, we characterized the cellular internalization and the kinetics of uptake of both types of polymersomes in different cell types (either cancer or non-cancer cells). We also investigated the cellular metabolic response as a function of the shape of the structures internalized and discovered that tubular vesicles induce a significant decrease in the replication activity of cancer cells compared to spherical vesicles. We related this effect to the significant up-regulation of the tumor suppressor genes p21 and p53 with a concomitant activation of caspase 3/7. Finally, we demonstrated that combining the intrinsic shape-dependent effects of tubes with the delivery of doxorubicin significantly increases the cytotoxicity of the system. Our results illustrate how the geometrical conformation of nanoparticles could impact cell behavior and how this could be tuned to create novel drug delivery systems tailored to specific biomedical application.
Direct and indirect effects of environmental factors, spatial constraints, and functional traits on shaping the plant diversity of montane forests
Understanding the relative importance of the factors driving the patterns of biodiversity is a key research topic in community ecology and biogeography. However, the main drivers of plant species diversity in montane forests are still not clear. In addition, most existing studies make no distinction between direct and indirect effects of environmental factors, spatial constraints on plant biodiversity. Using data from 107 montane forest plots in Sichuan Giant Panda habitat, China, we quantified the direct and indirect effects of abiotic environmental factors, spatial constraints, and plant functional traits on plant community diversity. Our results showed significant correlations between abiotic environmental factors and trees (r = 0.10, P value = 0.001), shrubs (r = 0.19, P value = 0.001), or overall plant diversity (r = 0.18, P value = 0.001) in montane forests. Spatial constraints also showed significant correlations with trees, and shrubs. However, no significant correlations were found between functional traits and plant community diversity. Moreover, the diversity (richness and abundance) of shrubs, trees, and plant communities was directly affected by precipitation, latitude, and altitude. Mean annual temperature (MAT) had no direct effect on the richness of tree and plant communities. Further, MAT and precipitation indirectly affected plant communities via the tree canopy. The results revealed a stronger direct effect on montane plant diversity than indirect effect, suggesting that single-species models may be adequate for forecasting the impacts of climate factors in these communities. The shifting of tree canopy coverage might be a potential indicator for trends of plant diversity under climate change.
Electrical impedance dataset of a thorax shaped tank
<p>This is a collection of Electrical Impedance Tomography measurements of a thorax cross-section shaped tank with 16 electrodes. These are published primarily for reproducibility and therefore the documentation is incomplete.</p> <p>CREDITS:<br> The measurements were carried out in 2012 by Aku Seppänen (University of Eastern Finland), Stratos Staboulis (Aalto University) and Nuutti Hyvönen (Aalto University). If you have questions about the data, please contact Nuutti Hyvönen (firstname.lastname@aalto.fi).<br> </p> <p>For information about the measurement device, please refer to:<br> Kourunen, J., Savolainen, T., Lehikoinen, A., Vauhkonen, M., and Heikkinen, L. M. - Suitability of a PXI platform for an electrical impedance tomography system. Meas. Sci. Technol. 20 (2009), 015503. DOI: 10.1088/0957-0233/20/1/015503<br> <br> For a general overview of the measurement setup, please refer to section 4.3 on:<br> Hyvönen, N., and Mustonen, L. - Smoothened electrode model. SIAM J. Appl. Math. 77 (2017), 2250–2271. DOI 10.1137/17M1124292<br> </p>
Data from: Association between nucleotide variation in Efgr and wing shape in Drosophila melanogaster
As part of an effort to dissect quantitative trait locus effects to the nucleotide level, association was assessed between 238 single-nucleotide and 20 indel polymorphisms spread over 11 kb of the Drosophila melanogaster Egfr locus and nine relative warp measures of wing shape. One SNP in a conserved potential regulatory site for a GAGA factor in the promoter of alternate first exon 2 approaches conservative experimentwise significance (P < 0.00003) in the sample of 207 lines for association with the location of the crossveins in the central region of the wing. Several other sites indicate marginal association with one or more other aspects of shape. No strong effects of sex or population of origin were detected with measures of shape, but two different sites were strongly associated with overall wing size in interaction with these fixed factors. Whole-gene sequencing in very large samples, rather than selective genotyping, would appear to be the only strategy likely to be successful for detecting subtle associations in species with high polymorphism and little haplotype structure. However, these features severely limit the ability of linkage disequilibrium mapping in Drosophila to resolve quantitative effects to single nucleotides.
Data from: Clade-age-dependent diversification under high species turnover shapes species richness disparities among tropical rainforest lineages of Bulbophyllum (Orchidaceae)
Background: Tropical rainforests (TRFs) harbour almost half of the world's vascular plant species diversity while covering only about 6–7% of land. However, why species richness varies amongst the Earth's major TRF regions remains poorly understood. Here we investigate the evolutionary processes shaping continental species richness disparities of the pantropical, epiphytic and mostly TRF-dwelling orchid genus Bulbophyllum (c. 1,948 spp. in total; Asia-Pacific region: c. 1,564 spp.; Madagascar: 210; Africa: 80; Neotropics: 94) using diversification analyses based on a time-calibrated molecular phylogeny, coupled with ecological niche modelling (ENM) of geographic distributions under present and past (Last Glacial Maximum) conditions. Results: Our results suggest an early-to-late Miocene scenario of 'out-of-Asia-Pacific' origin and progressive, dispersal-mediated diversification in Madagascar, Africa and the Neotropics, respectively. Species richness disparities amongst these four TRF lineages are best explained by a time-for-speciation effect rather than differences in net diversification or diversity-dependent diversification due to present or past spatial-bioclimatic limits. All four lineages of experienced dramatic range expansions during the LGM, which conflicts with the common notion that TRFs mostly fragmented/contracted during glacial periods. Conclusions: Most species of at least the Madagascan, African and Neotropical lineages originated during the Quaternary. Their diversification under high species turnover (i.e. high rates of speciation and extinction) might relate to climate-induced range fluctuations during this time period combined with various intrinsic features commonly invoked to foster rapid population turnover in tropical orchids (e.g., epiphytism, specialization on pollinators and mycorrhizal fungi, dispersal by wind). Further (e.g., phylogenomic and ecological) research within each Bulbophyllum lineage but also other pantropical TRF taxa is required to provide a better understanding of how evolutionary processes as well as past and current environmental conditions drive tropical biodiversity and account for regional differences in species richness patterns on a global scale.
Data from: Sex ratio variation shapes the ecological effects of a globally introduced freshwater fish
Sex ratio and sexual dimorphism have long been of interest in population and evolutionary ecology, but consequences for communities and ecosystems remain untested. Sex ratio could influence ecological conditions whenever sexual dimorphism is associated with ecological dimorphism in species with strong ecological interactions. We tested for ecological implications of sex ratio variation in the sexually dimorphic western mosquitofish, Gambusia affinis. This species causes strong pelagic trophic cascades and exhibits substantial variation in adult sex ratios. We found that female-biased populations induced stronger pelagic trophic cascades compared with male-biased populations, causing larger changes to key community and ecosystem responses, including zooplankton abundance, phytoplankton abundance, productivity, pH and temperature. The magnitude of such effects indicates that sex ratio is important for mediating the ecological role of mosquitofish. Because both sex ratio variation and sexual dimorphism are common features of natural populations, our findings should encourage broader consideration of the ecological significance of sex ratio variation in nature, including the relative contributions of various sexually dimorphic traits to these effects.
Data from: Epidermal growth factor receptor and transforming growth factor-ß signaling contributes to variation for wing shape in Drosophila melanogaster
Wing development in Drosophila is a common model system for the dissection of genetic networks and their roles during development. In particular, the RTK and TGF-ß regulatory networks appear to be involved with numerous aspects of wing development, including patterning, cell determination, growth, proliferation, and survival in the developing imaginal wing disc. However, little is known as to how subtle changes in the function of these genes may contribute to quantitative variation for wing shape, per se. In this study 50 insertional mutations, representing 43 loci in the RTK, Hedgehog, TGF-ß pathways, and their genetically interacting factors were used to study the role of these networks on wing shape. To concurrently examine how genetic background modulates the effects of the mutation, each insertion was introgressed into two wild-type genetic backgrounds. Using geometric morphometric methods, it is shown that the majority of these mutations have profound effects on shape but not size of the wing when measured as heterozygotes. To examine the relationships between how each mutation affects wing shape hierarchical clustering was used. Unlike previous observations of environmental canalization, these mutations did not generally increase within-line variation relative to their wild-type counterparts. These results provide an entry point into the genetics of wing shape and are discussed within the framework of the dissection of complex phenotypes.
Data from: Speciation rate is independent of the rate of evolution of morphological size, shape, and absolute morphological specialization in a large clade of birds
Whether ecological differences between species evolve in parallel with lineage diversification is a fundamental issue in evolutionary biology. These processes might be connected if conditions that favor the proliferation of species, such as release from competitors, facilitate the evolution of novel ecological relationships. Despite this, phylogenetic studies do not consistently identify such a connection. Conversely, if higher diversity caused species to become increasingly specialized ecologically, lineage diversification might become dissociated from ecological diversification. In this analysis, we ask whether the rate of lineage diversification in a large clade of birds is correlated with morphological specialization and with rates of morphological evolution. We find that morphological variation is related to species richness within clades, but that the rate of morphological evolution is decoupled from the rate of lineage diversification. Additionally, morphological specialization within lineages is independent of the rate at which lineages diversify, with the results apparently robust against false negative inference. This dissociation is likely a consequence of the major ecomorphological differences between avian clades arising early in their evolutionary history, with comparatively little variation added subsequently, while avian diversification has been driven predominantly by geographic isolation and sexual selection. Accordingly, biodiversity appears to be limited by the extent to which taxa can subdivide exploited regions of ecological space, and not just overall ecological opportunity.
Data from: Temperature shapes the costs, benefits, and geographic diversification of sexual coloration in a dragonfly
The environment shapes the evolution of secondary sexual traits by determining how their costs and benefits vary across the landscape. Given the thermal properties of dark coloration generally, temperature should crucially influence the costs, benefits, and geographic diversification of many secondary sexual color patterns. We tested this hypothesis using sexually selected wing coloration in a dragonfly. We find that greater wing coloration heats males—the magnitude of which improves flight performance under cool conditions but dramatically reduces it under warm conditions. In a colder region of the species' range, behavioral observations of a wild population show that these thermal effects translate into greater territorial acquisition on thermally variable days. Finally, geo-referenced photographs taken by citizen scientists reveal that this sexually selected wing coloration is dramatically reduced in the hottest portions of the species' range. Collectively, our results underscore temperature's capacity to promote and constrain the evolution of sexual coloration.
Data from: Horizontal and vertical diversity jointly shape food web stability against small and large perturbations
The biodiversity of food webs is composed of horizontal (i.e. within trophic levels) and vertical diversity (i.e. the number of trophic levels). Understanding their joint effect on stability is a key challenge. Theory mostly considers their individual effects and focuses on small perturbations near equilibrium in hypothetical food webs. Here, we study the joint effects of horizontal and vertical diversity on the stability of hypothetical (modelled) and empirical food webs. In modelled food webs, horizontal and vertical diversity increased and decreased stability, respectively, with a stronger positive effect of producer diversity on stability at higher consumer diversity. Experiments with an empirical plankton food-web, where we manipulated horizontal and vertical diversity and measured stability from species interactions and from resilience against large perturbations, confirmed these predictions. Taken together, our findings highlight the need to conserve horizontal biodiversity at different trophic levels to ensure stability.
Data from: Marine soundscape shaped by fishing activity
Marine communities face anthropogenic pressures that degrade ecosystems. Because underwater soundscapes carry information about habitat quality, we explored whether destructive impacts of fishing could be evaluated via the soundscape. Maerl beds are recognized as biodiversity hotspots and they experience major worldwide degradation owing to fishing. We collected field acoustic recordings in maerl beds exposed to different fishing practices. We found that unfished maerl beds were threefold louder and exhibited sound frequencies more diversified than those recorded in fished maerl beds. Analyses of associated fauna samples indicated that snapping shrimps provided a major contribution to the maerl bed soundscape. Moreover, sea urchins and squat lobsters most likely contributed to differences between the soundscapes of unfished and fished maerl beds. Our results supported the idea that the soundscape can provide valuable information on maerl bed ecosystem health related to fishing activity.
Data from: Size-dependent mortality and competition interactively shape community diversity
Body size is recognized as a major factor in evolutionary processes mediating sympatric diversification and community structuring. Life-history types with distinct body sizes can result from two fundamental mechanisms, size-dependent competition and size-dependent mortality. While previous theoretical studies investigated these two processes in separation, the model analyzed here allows both selective forces to affect body-size evolution interactively. Here we show for the first time that in the presence of size-dependent competition, size-dependent mortality can give rise to multiple, coexisting size morphs representing the final outcomes of evolution. Moreover, our results demonstrate that interactions between size-dependent competition and mortality can create characteristic abrupt changes in size structure and non-monotonic patterns of biological diversity along continuous and monotonic environmental gradients. We find that the two selective forces differentially affect the body-size ratios of coexisting morphs: size-dependent competition results in small and relatively constant ratios, whereas size-dependent mortality can open niches for morphs that greatly differ in body size. We show that these differential effects result in characteristic distributions of size ratios across communities, which we suggest can help detect the concurrent action and relative influence of size-dependent competition and mortality in nature.
Data from: Early bursts of body size and shape evolution are rare in comparative data
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.
Figure 4 from: Vujić V, Lučić L, Pavković-Lučić S, Ilić B, Jovanović Z, Makarov S, Dudić B (2020) Sexual size and shape dimorphism in Brachydesmus troglobius Daday, 1889 (Diplopoda, Polydesmida). In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 75-88. https://doi.org/10.3897/zookeys.930.48285
Figure 4 Intersexual differences in CS of: A antennae B heads C legs.
Garnet 3D grain shapes in the metabasalt ZS-21-02
<p>This dataset is part of the Supplemental Material of "<strong>Tracking garnet dissolution kinetics in 3D using deep learning grain shape classification</strong>" by Hartmeier et al. (2023).</p><p>Garnet grain 3D models extracted from a micro-computed tomography scan. "<i>ZS2102raw" are numpy arrays (.npy-files) holding a 3D model of garnet grains. Additional information; centroid position, volume in voxels and volume of fitted convex hulls ; is stored in seperate files. "ZS2102_labelled" </i>holds the same data set but all garnets are catergorised in to different shape based classes.</p>
Climate anomalies and neighbourhood crowding interact in shaping tree growth in old-growth and selectively-logged tropical forests
<p>Species mean information for the six leaf water-related traits used in the paper titled: Climate anomalies and neighbourhood crowding interact in shaping tree growth in old-growth and selectively-logged tropical forests.</p>
Etrog dish with a leaf-shaped tray
Creator: Friedrich Wilhelm Sponholtz (1730–1789) Time and place of creation: ca. 1772, Gdańsk, Poland Jagiellonian University Museum Collegium Maius Inventory number: 9310/1–2; 1542/IV; 1543/IV https://muzea.malopolska.pl/en/objects-list/2743 Source: Objaverse 1.0 / Sketchfab
Fig 3 from: Heller K-G, Hemp C (2024) Egg shape and size in Phaneropterinae and other Tettigonioidea (Orthoptera, Ensifera): A global review with new data. Journal of Orthoptera Research 33(1): 103-112. https://doi.org/10.3897/jor.33.116173
Fig 3 Dimensions of eggs in different phaneropterine tribes.
Data from: Development, feeding, and sex shape the relative quantity of the nutritionnal obligatory symbiont Wolbachia in bed bugs
<p>Datasets and scripts (statistical analyses and graphs) from "Development, feeding, and sex shape the relative quantity of the nutritionnal obligatory symbiont <em>Wolbachia</em> in bed bugs" by Poulain <em>et al.</em>, <em>Frontiers in Microbiology</em>, 15:1386458.</p> <p>doi: 10.3389/fmicb.2024.1386458</p>
Data about "The individual training history shapes soccer players' ability to predict teammates' and opponents' moves"
<p>This repository contains the data related to the two experiments presented in the article: <em>"The individual training history shapes soccer players' ability to predict teammates' and opponents' moves."</em> In addition to the accuracy scores of individual players, data on the soccer experience of the participants are also provided. Finally, the videos used as stimuli in the experimental procedure are included. The videos depict a soccer player performing typical actions for different positions on the field, which are stopped before the completion of the movement.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.